San Francisco quarterback Colin Kaepernick (7) runs for a 56-yard touchdown in the third quarter against the Green Bay Packers in the NFC divisional playoff on Saturday, January 12, 2013, at Candlestick Park in San Francisco, Calif. (Jim Gensheimer/San Jose Mercury News/MCT)

After drafting roughly half the world’s supply of defensive players in April, the Green Bay Packers thought they had their defense fixed.

They thought wrong.

For the third time in four years, the Packers were eliminated from the NFL playoffs earlier than expected, this time with a 45-31 road loss to the San Francisco 49ers on Saturday night, Jan. 12.

The game was the latest in a string of defensive meltdowns in the playoffs that was interrupted only by the Packers’ run to the NFL title two years ago. At this point, that marvelous defensive performance in 2010, not unlike the Packers themselves, looks more like a snapshot than a photo album.

In losing to Arizona in the 2009 playoffs, the Packers gave up 51 points and 531 yards. In 2011, they allowed 37 points and 420 yards to the New York Giants. They hit a new low Saturday, surrendering 45 points and a mind-boggling 579 yards to the 49ers, including 323 on the ground.

In the past, the Packers couldn’t counter the passing of Arizona’s Kurt Warner and New York’s Eli Manning. On Saturday, they had no answers for the running and passing of 6-foot-4, 230-pound Colin Kaepernick, a second-year man who dominated the game with his blazing speed and uncommon accuracy for a running quarterback.

That’s the scary part as the Packers look to their future. Like Washington’s Robert Griffin III, Seattle’s Russell Wilson and Carolina’s Cam Newton, Kaepernick is a new-age quarterback who can burn opponents using college-style read-option runs, scrambling with a run-first mentality and throwing with power and accuracy.

After two decisive losses to the 49ers this season, the Packers clearly have fallen behind them in the NFC. And with Seattle and Washington also making advances in the NFC, the Packers will have to make defensive changes in a league that is evolving before our eyes.

“For years, they said it couldn’t be done,” safety Charles Woodson said. “They said the defenses were too fast. But you see a lot of young, athletic quarterbacks coming in that can run that zone read-option. The more athletic guys you bring in, the more coaches you bring in that coach it, it’s hard to stop.”

Hard for most, impossible for the Packers. Kaepernick rushed 16 times for 181 yards, which broke Michael Vick’s record for the most rushing yards by a quarterback in an NFL game, postseason or otherwise.

In a startling number from ESPN Stats, Kaepernick gained 178 of his 181 yards before contact. Green Bay tried using a spy on him at times and blitzed him on other occasions, but the Packers were so confused they couldn’t even lay a hand on him.

Sure, the 49ers fooled the Packers. Kaepernick was making only his eighth NFL start and the 49ers had used read-option plays only about 10 times previously. On Saturday, they lined up in the pistol formation about half the time and used the read-option extensively.

Still, the Packers’ inability to get a handle on Kaepernick raised some serious concerns. Are they fast or physical enough on defense? Has coordinator Dom Capers run out of adjustments to make against teams with running threats at quarterback?

Despite the influx of useful rookies, the Packers aren’t yet physical enough on defense. Kaepernick said his job was easy because the 49ers line “dominated up front.” However, the lack of a physical presence on the defense was more evident at linebacker and in the secondary than it was up front.

The Packers also lack the playmaking speed they had on defense in 2010. Safety Nick Collins was forced into early retirement and Woodson isn’t the player he once was after 15 NFL seasons. With no equivalent replacements, linebacker Clay Matthews is the only real playmaker on defense.

“We’ve just got to get better,” Woodson said. “I look at this team we just played and they’re a big, fast team. I think as far as our team is concerned, and I don’t know what happens here going forward, but we’ve got to get bigger and faster.”

And tougher?

“I don’t think we have a problem toughness-wise,” Woodson said. “But we just ran into a team that was a very deep team. Watching them defensively, they were everywhere. It seemed like we didn’t have a lot of holes there to make things happen. … Then with the (49ers) offense, what they were able to do with the plays they were running for the quarterback, him getting out of the pocket, him making plays with his feet and then making some throws. It was hard to be a part of.”

Despite the personnel issues, it is fair to question Capers’ future, too. He has been coaching Pittsburgh’s 3-4 zone-blitz scheme with great success for more than 20 years, but the new wave of running quarterbacks might be making that style obsolete.

Woodson and several others said Capers didn’t make any adjustments Saturday. However, maybe there were no adjustments to make.

“I just think when the game is going the way it is, you’ve got to try something different,” Woodson said. “It’s hard to just continue to do the same thing over and over again, and continue to get burned. … We need to figure out: Could we have done something differently as far as our game plan was concerned?”

The Packers need to do something different on defense, period, and they need to do it quickly because their window of opportunity with quarterback Aaron Rodgers won’t last forever.

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